8000 BUG: Segmentation fault when working with open3d · Issue #26853 · numpy/numpy · GitHub
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AlterraFa opened this issue Jul 4, 2024 · 6 comments
Closed

BUG: Segmentation fault when working with open3d #26853

AlterraFa opened this issue Jul 4, 2024 · 6 comments
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00 - Bug

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@AlterraFa
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AlterraFa commented Jul 4, 2024 •
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Describe the issue:

I encountered a segmentation fault when drawing using open3d
There are 2 variables XYZ and XYZreformat
However XYZ give a segmentation fault, even when I reassign its data type to float64 by using XYZ = XYZ.astype(np.float64)
Only the code below works

Note: The older version seems to work but not with the version 2.0.0
depth.csv

Reproduce the code example:

import scipy.io.matlab as mat
import numpy as np
import open3d as o3d
import pandas as pd
import faulthandler
faulthandler.enable()

depth_arr = pd.read_csv('depth.csv').to_numpy()

sx = 32 / 1024 # Ratio between sensor width and total pixel. Assume sx = sy
fx = 24 / sx
fy = 24 / sx
Cx = 1024 // 2 - 1
Cy = 512 // 2 - 1

# x and y coordinates
x = np.arange(0, 1024, 1)
y = np.arange(0, 512, 1)

x, y = np.meshgrid(x, y, copy = True) # Meshgrid for x and y. This is 2D array
u, v = x - Cx, y - Cy # calculate distance from center the center   X\
    

Z = depth_arr / (((u / fy) ** 2 + (v / fx) ** 2 + 1) ** .5) # Calculate depth array
Zravel = Z.ravel() # convert from 2D to 1D array

kernel = np.array([[1 / fx, 0, -Cx / fx],
                   [0, 1 / fy, -Cy / fy],
                   [0, 0, 1]]) # Kernel or transfer function of vector [X / Z, Y / Z, 1]

xravel = x.ravel() # convert from 2D to 1D array
yravel = y.ravel() # convert from 2D to 1D array



# create an array containing x, y coordinates
# This will result in an array that looks like this:
# [[x1, x2, x3, ..., xn],
#  [y1, y2, y3, ..., yn],
#  [1, 1, 1, ..., 1]]
# Instead of doing for loop with
# [[X / Z],
#  [Y / Z],
#  [1]]
# = kernel dot product with
# [[x],

#  [y],
#  [1]]
# We can use the afformentioned array to instead calculate the dot product between kernel and the above array
xy_vector = np.array([xravel, yravel, np.ones_like(xravel)]) 
resultant_3d_vector = kernel @ xy_vector # @ is also the dot product operation
# print(resultant_3d_vector)
XYZ = (resultant_3d_vector * Zravel).T # transpose for compatibility with open3d input array [[X, Y, Z]]
XYZreformat = np.array(XYZ.tolist(), dtype = np.float64)


if __name__ == "__main__":
    pcd = o3d.geometry.PointCloud()
    pcd.points = o3d.utility.Vector3dVector(XYZ)
    o3d.visualization.draw_geometries([pcd])

Error message:

Fatal Python error: Segmentation fault

Current thread 0x00007ad4343be000 (most recent call first):
  File "/mnt/6208995F089932D1/Coding/Python/Realsense Example/pointcloudpractice.py", line 61 in <module>

Extension modules: numpy._core._multiarray_umath, numpy._core._multiarray_tests, numpy.linalg._umath_linalg, scipy._lib._ccallback_c, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, charset_normalizer.md, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.io.matlab._mio_utils, scipy.io.matlab._streams, scipy.io.matlab._mio5_utils, markupsafe._speedups, zmq.backend.cython._zmq, tornado.speedups, psutil._psutil_linux, psutil._psutil_posix, _brotli, simplejson._speedups, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing (total: 90)
Segmentation fault (core dumped)

Python and NumPy Versions:

2.0.0
3.10.12 (main, Nov 20 2023, 15:14:05) [GCC 11.4.0]

Runtime Environment:

[{'numpy_version': '2.0.0',
'python': '3.10.12 (main, Nov 20 2023, 15:14:05) [GCC 11.4.0]',
'uname': uname_result(system='Linux', node='alterraonix-LOQ', release='6.5.0-41-generic', version='#41~22.04.2-Ubuntu SMP PREEMPT_DYNAMIC Mon Jun 3 11:32:55 UTC 2', machine='x86_64')},
{'simd_extensions': {'baseline': ['SSE', 'SSE2', 'SSE3'],
'found': ['SSSE3',
'SSE41',
'POPCNT',
'SSE42',
'AVX',
'F16C',
'FMA3',
'AVX2'],
'not_found': ['AVX512F',
'AVX512CD',
'AVX512_KNL',
'AVX512_KNM',
'AVX512_SKX',
'AVX512_CLX',
'AVX512_CNL',
'AVX512_ICL']}},
{'architecture': 'Haswell',
'filepath': '/home/alterraonix/.local/lib/python3.10/site-packages/numpy.libs/libscipy_openblas64_-99b71e71.so',
'internal_api': 'openblas',
'num_threads': 12,
'prefix': 'libscipy_openblas',
'threading_layer': 'pthreads',
'user_api': 'blas',
'version': '0.3.27'}]

Context for the issue:

This might lead to other problems since this is a segmentation fault with another library so I reported it
@seberg
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seberg commented Jul 4, 2024

This is not an issue with NumPy, please search the issues at open3d (or open one there). You can try downgrading NumPy to numpy<2 if you think that is a new issue. But it would be strange if it makes a difference (i.e. compiled for NumPy 2, even though it is not yet supported).

@seberg seberg closed this as not planned Won't fix, can't repro, duplicate, stale Jul 4, 2024
@Wendyiii
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Have you solved this problem? I'm also having the same issue, can you tell me what to do？Thank you veeeeeery much

@AlterraFa
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Have you solved this problem? I'm also having the same issue, can you tell me what to do？Thank you veeeeeery much

Yeah, by downgrading it to numpy < 2.0.0

@Wendyiii
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Great, this method worked, thank you again!!!

@antoinekeller
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Same here, downgrading to numpy==1.26.4 solved my issue

@mattip
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mattip commented Aug 29, 2024

A quick search for "numpy" and "segmentation" leads to many open issues in that project. Unless we can get a clearer reproducer, I am going to assume the crash is in open3d. This issue is closed, please do not add more comments here.

@umutcanustuntas umutcanustuntas mentioned this issue Oct 1, 2024
Open
@B1ueber2y B1ueber2y mentioned this issue Jan 6, 2025
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@seberg @mattip @antoinekeller @AlterraFa @Wendyiii
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